Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.1.1.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06478	0.904
27DAP/17DAP	0.93562	0.889
39DAP/27DAP	1.06926	1
41DAP/39DAP	0.77493	0.258
42DAP/41DAP	1.01623	1
43DAP/42DAP	1.13013	1
47DAP/43DAP	0.92787	0.736
52DAP/47DAP	0.80414	0.518
57DAP/52DAP	1.07112	0.902

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09861	0.147
17DAP/reference	1.03649	0.33
27DAP/reference	0.92309	0.163
39DAP/reference	1.02731	0.534
41DAP/reference	1.01311	0.714
42DAP/reference	1.12599	0.299
43DAP/reference	0.98064	0.675
47DAP/reference	1.04911	0.627
52DAP/reference	0.96409	0.35
57DAP/reference	0.88161	0.04

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.977	0.75
27DAP/17DAP	0.94824	0.684
39DAP/27DAP	0.87863	0.058
41DAP/39DAP	1.03777	0.914
42DAP/41DAP	1.07442	0.824
43DAP/42DAP	0.90367	0.246
47DAP/43DAP	0.98368	0.93
52DAP/47DAP	1.5295	0.106
57DAP/52DAP	1.54069	0.054
57DAP/7DAP	0.99174	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8675	0.095
17DAP/reference	0.94664	0.389
27DAP/reference	1.13682	0.049
39DAP/reference	0.75713	0.023
41DAP/reference	0.70749	0.022
42DAP/reference	0.78468	0.034
43DAP/reference	0.90302	0.121
47DAP/reference	0.94339	0.504
52DAP/reference	1.13422	0.832
57DAP/reference	0.8627	0.064

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03292	0.951
17DAP/reference	1.17924	0.049
27DAP/reference	1.26176	0.044
39DAP/reference	1.25106	0.207
41DAP/reference	1.1671	0.162
42DAP/reference	1.22717	0.068
43DAP/reference	1.31517	0.054
47DAP/reference	1.08533	0.24
52DAP/reference	1.24739	0.006
57DAP/reference	1.30478	0.057

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88934	0.214
17DAP/reference	1.31971	0.096
27DAP/reference	1.12319	0.271
39DAP/reference	1.07529	0.33
41DAP/reference	1.11852	0.734
42DAP/reference	1.1237	0.246
43DAP/reference	1.13128	0.49
47DAP/reference	1.23966	0.008
52DAP/reference	1.13286	0.272
57DAP/reference	1.2464	0.187

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85034	0.981
26DAP/20DAP	1.0693	1
34DAP/26DAP	1.76917	0.819
51DAP/34DAP	1.03778	0.747
52DAP/51DAP	2.12235	0.051
53DAP/52DAP	0.73786	0.062
55DAP/53DAP	1.44232	0.039
57DAP/55DAP	0.68044	0.123
62DAP/57DAP	0.61614
68DAP/62DAP	0.87201	0.345
68DAP/14DAP	0.78224	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.42046	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.05097	0.176
Mature Green Tomato/Ripe Tomato	2.09533	0.044
Immature Eggplant/Mature Eggplant	0.63738	0.068
Ripe Pepper/Ripe Tomato	1.40895	1
Mature Eggplant/Ripe Tomato	1.051	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.91566	1
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	1.91974
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.11564	1
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.77879
4-3-2/M82	1.45318
4-3/M82	N/A	N/A
5-3/M82	1.21589	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.18361	0.196

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93353	1
IL2-6/WTpooled	1.41188	0.427
IL7-5/WTpooled	1.21097	1
IL7-3/WTpooled	0.94747	1
IL12-4/WTpooled	0.93546	0.71
IL1-4/WTpooled	1.06524	0.426
WT/WTpooled	1.08801	0.999

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.16667	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.09945	1
DC3000/delta hrp 6h	1.10146	1
DC3000/delta hrp 12h	1.87259	1
DC3000/delta hrp 24h	0.82936	0.121

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1735	0.042
DC3000 delta B/DC3000 delta AB	1.26453	0.246

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.05103	1
Exp 36h	0.92883	0.749
Exp 60h	0.92	0.754

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	1.03571	1
Var 0h	0.91481	0.933
Var 12h I row2-row1	0.75741	0.357
Var 12h NI row2-row1	0.99204	1
Var 36h I row2-row1	1.0277	1
Var 36h NI row2-row1	1.28621	0.276
Var 60h I row2-row1	0.77967	0.374
Var 60h NI row2-row1	1.03344	1
Time course 0hI-0hNI	0.94593	0.618
Time course 12hI-12hNI	0.9609	0.746
Time course 36hI-36hNI	0.81776	0.026
Time course 60hI-60hNI	0.50248	0.006

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.07846	0.541
transgenic ySAMdc/azygous control (breaker)	1.40285	0.166
transgenic ySAMdc/azygous control (red)	1.05178	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.98904	0.5

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.33848	0.233

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.78132	0.083
Manapal/WT (break)	1.61861	0.14
Manapal/WT (red)	1.38351	0.413